The differences between ground and transition state properti
The differences between ground and transition state properties are exemplified by a comparison of our human–yeast results with those of a structural study of possible differences in ubiquitin-Uba-1 binding in yeast (known structure) with human (simulated in ). Their discussion focuses on Ubiquitin contacts with Tyr 571 (618 in our site numbering) in the CCD domain. According to Fig. 3 and its caption, there are substantial differences between yeast and human profiles here, and they are related to differences in tilts of the hydrophobic pivots. These are consistent with the modeling results, and also show the importance of allometric interactions between folded CC and CCD domains (Fig. 5).
Human AAD adenylation (ATP) sites are 478, 504, 515, and 528. The overall BLAST identities and positives for yeast and human Uba1 are 52% and 71%, and these increase in the 400–600 ADD range to 63% and 80%. This range is shown in Fig. 6, and we see strong similarities in the two profiles. Their correlation is 86%, which means that is more effective in the 400–600 ADD range than even BLAST positives (80%) because it uses the MZ scale and because W* has been chosen to display level set hydrophobic adenylation domain pivots. From Fig. 6 we see that the four sites are concentrated in the center of the ADD structural domain. They line the amphiphilic range from the hydrophobic pivot at 478 to close to the ergosterol hinge at 535. The profile not only displays a stronger yeast–human ADD correlation than BLAST, but it also has revealed a hydropathic cascade of ATP binding sites. Among mammals the similarities are of course greater. The overall correlation of the mouse and human profiles is 97.2%, which increases in the 400–600 ADD range to 98.6 %.
There has recently been some interest in Uba6, which is most similar to slime mold, with BLAST identities of 59% and positives 73% in the 400–600 ADD range. The 400–600 ADD correlation of the two profiles is a striking 87%, so functional differences probably arise outside the ADD binding domain. Human Uba6 and Uba1 have distinct preferences for E2 charging in vitro, and their specificity depends in part on their C-terminal ubiquitin-fold domains, which recruit E2s . Comparison of Uba1 of yeast and slime mold with Uba6 shows that for the most part, where Uba6 differs from one of the two, it is similar to the other. The exceptional region is UFD, the ubiquitin fold domain (Fig. 5), where Uba6 has a strong hydrophobic peak. Similar differences are obvious in the human and fruit fly profiles. This “only” confirms the main conclusion of , but note that it does so through a simple one-dimensional analysis that also includes many species’ versions of Uba1.
Conclusions At present the most sophisticated structural studies involving MDS simulations with explicit water  can reveal short-range interspecies differences in Uba-E1 — Ub binding, but long-range interactions are not identified. Proteins are near thermodynamic critical points in amino acid configuration space, and near such points (especially transition states), long-range and short-range interactions are balanced. In many proteins the short-range interactions evolve in subtle ways inaccessible to experiment, while here we have shown that the long-range interactions change in ways that can be easily recognized in . Evolutionary trends are easily recognized by thermodynamic scaling theory.
Main Text Posttranslational attachment of ubiquitin (Ub), a small 76-residue protein, is one of the most abundant protein modifications in eukaryotic cells. The process of ubiquitination, covalently linking the C terminus of Ub to a lysine ε-amine on a protein substrate, is carried out through a three-enzyme cascade (E1, E2, E3; Figure 1A). In the case of polyubiquitination, additional Ub molecules can be attached at eight positions (M1, K6, K11, K27, K29, K33, K48, or K63) on the previously linked Ub molecule, resulting in diverse polymeric Ub chains (Glickman and Ciechanover, 2002). This property enables polyUb chains to form distinct signals and hence the broad range of polyUb signaling pathways. As a mechanism to reverse ubiquitination, deubiquitinating enzymes (DUBs) act to depolymerize polyUb back to monomeric units and also remove the proximal Ub from substrates (Komander et al., 2009). Through tight regulation of ubiquitination cascades and DUBs, cells maintain a viable balance between free Ub and substrate-attached Ub.